I’m not sure that have the answers to the why questions you want.
I can say that, with only an available .ENL file, because most of the overhaul to the EndNote Library structure are the underlying .DATA files/indexes, a missing .DATA folder is going to prevent the EndNote software from being able to tell whether it’s the new format, or the old. Whenever possible, users should open the EndNote with the .DATA folder present, as it really contains the bulk of the data for the library. It’s not uncommon for an .ENL to have a 0KB file size, as the .ENL file is really a portal into the indexes contained within the .DATA folder.
I can speak to the multiple shared library issue, as it is possible for inter-sharing to help with that.
By which, I mean that each user can share a library.
Sharing is limited to synchronizing 1 library per user. This means that if you have 4 users, potentially you can share 4 different libraries, presuming the users aren’t Synchronizing a personal collection.
The library location issues are mostly speed of access, and simultanous access issues.
Used responsibly, and taking care that no other process is attempting to access/copy/scan EndNote library indexes while the library is in use would definitely help to ensure that the library data remains undamaged.
I mention it because many users aren’t nearly as responsible with their EndNote library files, and get into serious trouble.
I really can’t stress enough that we should be contacted if there are any concerns, or questions, whether or not hold a license for EndNote themselves. When performing any function that may give a user cause for confusion or doubt, we’re available in Technical Support to help answer the question.
https://support.clarivate.com/Endnote/s/?language=en_US
Monday thru Friday, 24/5 we’re available, email, chat, and phone.
And thanks again for your support, and all your help with the forums.
Steve